nCal: an R package for non-linear calibration

Fong, Youyi; Sebestyen, Krisztian; Yu, Xuesong; Gilbert, Peter B.; Self, Steve

doi:10.1093/bioinformatics/btt456

Cited by 24 publications

(19 citation statements)

References 2 publications

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“…The numerical problem of fitting a 5PL model has been well documented (Seber and Wild, 1989;Ratkowsky, 1990Ratkowsky, , 1986. From our experience, this problem can be alleviated to a degree by allowing the optimization routine to try several methods when choosing the initial values, e.g., as implemented in the R package nCal (Fong et al, 2013). That our Monte Carlo studies use no knowledge about the simulation truth in the optimization process suggests the algorithm implemented therein is suitable for practical use.…”

Section: Discussionmentioning

confidence: 99%

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Nonlinear Calibration Model Choice between the Four and Five-Parameter Logistic Models

Cumberland

Fong

et al. 2014

Journal of Biopharmaceutical Statistics

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Both the four-parameter logistic (4PL) and the five-parameter logistic (5PL) models are widely used in nonlinear calibration. In this paper, we study the choice between 5PL and 4PL both by the accuracy and precision of the estimated concentrations and by the power to detect an association between a binary disease outcome and the estimated concentrations. Our results show that when the true curve is symmetric around its inflection point, the efficiency loss from using 5PL is negligible under the prevalent experimental design. When the true curve is asymmetric, 4PL may sometimes offer better performance due to bias-variance trade-off. We provide a practical guideline for choosing between 5PL and 4PL and illustrate its application with a real dataset from the HIV Vaccine Trials Network laboratory.

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Section: Discussionmentioning

confidence: 99%

“…We will use the maximum likelihood method to estimate the parameters of the logistic model using the R packages nCal (Fong et al, 2013) and drc (Ritz and Streibig, 2005). Letθ denote the parameter estimate, and let Fθ denote the estimated concentration-response function.…”

Section: Calibration Performancementioning

confidence: 99%

Nonlinear Calibration Model Choice between the Four and Five-Parameter Logistic Models

Cumberland

Fong

et al. 2014

Journal of Biopharmaceutical Statistics

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“…Lysate buffer was used for background measurements in the skin panel; RPMI with 20% FBS was used for the cytokine panel. Curve fitting for MBA standards used the nCal R package [42] . Extrapolated data from the MBA was analyzed using the ratio of inner versus outer analyte concentrations.…”

Section: Methodsmentioning

confidence: 99%

The Inner Foreskin of Healthy Males at Risk of HIV Infection Harbors Epithelial CD4+ CCR5+ Cells and Has Features of an Inflamed Epidermal Barrier

et al. 2014

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Male circumcision provides partial protection against multiple sexually transmitted infections (STIs), including HIV, but the mechanisms are not fully understood. To examine potential vulnerabilities in foreskin epithelial structure, we used Wilcoxon paired tests adjusted using the false discovery rate method to compare inner and outer foreskin samples from 20 healthy, sexually active Peruvian males who have sex with males or transgender females, ages 21–29, at elevated risk of HIV infection. No evidence of epithelial microtrauma was identified, as assessed by keratinocyte activation, fibronectin deposition, or parakeratosis. However, multiple suprabasal tight junction differences were identified: 1) inner foreskin stratum corneum was thinner than outer (p = 0.035); 2) claudin 1 had extended membrane-bound localization throughout inner epidermis stratum spinosum (p = 0.035); 3) membrane-bound claudin 4 was absent from inner foreskin stratum granulosum (p = 0.035); and 4) occludin had increased membrane deposition in inner foreskin stratum granulosum (p = 0.042) versus outer. Together, this suggests subclinical inflammation and paracellular transport modifications to the inner foreskin. A setting of inflammation was further supported by inner foreskin epithelial explant cultures secreting higher levels of GM-CSF (p = 0.029), IP-10 (p = 0.035) and RANTES (p = 0.022) than outer foreskin, and also containing an increased density of CCR5+ and CD4+ CCR5+ cells (p = 0.022). Inner foreskin dermis also secreted more RANTES than outer (p = 0.036), and had increased density of CCR5+ cells (p = 0.022). In conclusion, subclinical changes to the inner foreskin of sexually active males may support an inflammatory state, with availability of target cells for HIV infection and modifications to epidermal barriers, potentially explaining the benefits of circumcision for STI prevention.

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“…Normalized intensities were then scaled to the mean reactivity for each antigen to allow comparison between antigens. Using the ncal function within the nCal package(61), IgG concentrations were interpolated from the standard curves generated from serial diluted pooled malaria-immune plasma and the resulting concentrations reported as arbitrary units (AU), which was used for statistical analyses and visualization.…”

Section: Methodsmentioning

confidence: 99%

Longitudinal analysis of naturally acquired antibodies to PfEMP1 CIDR domain variants and their association with malaria protection

Obeng-Adjei

Larremore

Turner

et al. 2020

Preprint

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Malaria pathogenicity is determined, in part, by the adherence of Plasmodium falciparum infected erythrocytes to the microvasculature mediated via specific interactions between PfEMP1 variant domains to host endothelial receptors. Naturally acquired antibodies against specific PfEMP1 variants can play an important role in clinical protection against malaria. We evaluated IgG responses against a repertoire of PfEMP1 CIDR domain variants to determine the rate and order of variant-specific antibody acquisition and their association with protection against febrile malaria in a prospective cohort study conducted in an area of intense, seasonal malaria transmission. Using longitudinal data, we found that IgG to the pathogenic domain variants CIDRα1.7 and CIDRα1.8 were acquired the earliest. Furthermore, IgG to CIDRγ3 was associated with reduced prospective risk of febrile malaria and recurrent malaria episodes. Future studies will need to validate these findings in other transmission settings and determine the functional activity of these naturally acquired CIDR variant-specific antibodies.

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nCal: an R package for non-linear calibration

Abstract: The R package 'nCal' is available from http://cran.r-project.org/web/packages/nCal/ under GPL-2 or later.

Cited by 24 publications

References 2 publications

Nonlinear Calibration Model Choice between the Four and Five-Parameter Logistic Models

Nonlinear Calibration Model Choice between the Four and Five-Parameter Logistic Models

The Inner Foreskin of Healthy Males at Risk of HIV Infection Harbors Epithelial CD4+ CCR5+ Cells and Has Features of an Inflamed Epidermal Barrier

Longitudinal analysis of naturally acquired antibodies to PfEMP1 CIDR domain variants and their association with malaria protection

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